This study aimed to compare the protective role a crude mixture of thyme and basil essential oils (TO and BO) and their nanoemulsion (TON and BON) against oxidative damage, cytotoxicity and DNA fragmentation in rats exposed to titanium dioxide nanoparticles (TiO2-NPs). Six groups of male Sprague-Dawley rats were subjected to oral treatment for 3 weeks including, the control group, the group treated with TO plus BO (5 mg/kg b.w each), the group treated with TON plus BON (2.5 mg/kg b.w each), the group treated with TiO2-NPs (50 mg/kg b.w) and the groups treated with TiO2-NPs plus the TO and BO or TON plus BON. Blood and tissue samples were collected for different bioassays, cytogenetic and histological examination. The results revealed that TiO2-NPs disturbed the liver and kidney indices, lipid profile, serum cytokines oxidant/antioxidant markers, antioxidant gene expression and histological structure in the liver. Both TO plus BO or TON plus BON could prevent these disturbances and TON plus BON were more effective. These outcomes indicated the synergistic effect of the oils and the role of nanoemulsion in the enhancement of the antioxidant efficiency beside expand their dispersibility and foster their controlled delivery in addition to the antioxidant property of WPI. It could be concluded that TON and BON are safe and can be applied for the preparation of eco-friendly antioxidant for food and medical purposes.